Starting phenix.real_space_refine on Sun Mar 10 21:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/03_2024/7zky_14771.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/03_2024/7zky_14771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/03_2024/7zky_14771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/03_2024/7zky_14771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/03_2024/7zky_14771.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/03_2024/7zky_14771.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3324 2.51 5 N 930 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 47": "NH1" <-> "NH2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5238 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "A" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "D" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "H" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "G" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "J" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "I" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "L" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Time building chain proxies: 3.33, per 1000 atoms: 0.64 Number of scatterers: 5238 At special positions: 0 Unit cell: (71.76, 109.2, 50.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 960 8.00 N 930 7.00 C 3324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 2.2 seconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.981A pdb=" N TYR B 42 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR D 42 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR F 42 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR H 42 " --> pdb=" O ASP J 43 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR J 42 " --> pdb=" O ASP L 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 55 through 58 removed outlier: 6.813A pdb=" N ALA B 55 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE D 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 57 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA D 55 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE F 58 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA D 57 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA F 55 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE H 58 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA F 57 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA H 55 " --> pdb=" O GLU J 56 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE J 58 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA H 57 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA J 55 " --> pdb=" O GLU L 56 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE L 58 " --> pdb=" O ALA J 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA J 57 " --> pdb=" O ILE L 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 68 Processing sheet with id=AA4, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.687A pdb=" N TYR A 35 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 35 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 35 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR G 35 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR I 35 " --> pdb=" O PHE K 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 25 hydrogen bonds defined for protein. 75 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 868 1.32 - 1.44: 1874 1.44 - 1.56: 2604 1.56 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5394 Sorted by residual: bond pdb=" CA SER E 32 " pdb=" CB SER E 32 " ideal model delta sigma weight residual 1.526 1.475 0.051 1.26e-02 6.30e+03 1.61e+01 bond pdb=" CA SER K 32 " pdb=" CB SER K 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.58e+01 bond pdb=" CA SER A 32 " pdb=" CB SER A 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.58e+01 bond pdb=" CA SER I 32 " pdb=" CB SER I 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.58e+01 bond pdb=" CA SER G 32 " pdb=" CB SER G 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.57e+01 ... (remaining 5389 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.56: 295 107.56 - 114.30: 2217 114.30 - 121.03: 2835 121.03 - 127.77: 1817 127.77 - 134.50: 54 Bond angle restraints: 7218 Sorted by residual: angle pdb=" N ARG H 62 " pdb=" CA ARG H 62 " pdb=" C ARG H 62 " ideal model delta sigma weight residual 112.90 105.55 7.35 1.31e+00 5.83e-01 3.15e+01 angle pdb=" N ARG B 62 " pdb=" CA ARG B 62 " pdb=" C ARG B 62 " ideal model delta sigma weight residual 112.90 105.58 7.32 1.31e+00 5.83e-01 3.12e+01 angle pdb=" N ARG L 62 " pdb=" CA ARG L 62 " pdb=" C ARG L 62 " ideal model delta sigma weight residual 112.90 105.58 7.32 1.31e+00 5.83e-01 3.12e+01 angle pdb=" N ARG J 62 " pdb=" CA ARG J 62 " pdb=" C ARG J 62 " ideal model delta sigma weight residual 112.90 105.58 7.32 1.31e+00 5.83e-01 3.12e+01 angle pdb=" N ARG D 62 " pdb=" CA ARG D 62 " pdb=" C ARG D 62 " ideal model delta sigma weight residual 112.90 105.61 7.29 1.31e+00 5.83e-01 3.10e+01 ... (remaining 7213 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.55: 2737 17.55 - 35.10: 215 35.10 - 52.65: 54 52.65 - 70.20: 12 70.20 - 87.75: 12 Dihedral angle restraints: 3030 sinusoidal: 1206 harmonic: 1824 Sorted by residual: dihedral pdb=" CA ASP L 60 " pdb=" CB ASP L 60 " pdb=" CG ASP L 60 " pdb=" OD1 ASP L 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.95 57.95 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP F 60 " pdb=" CB ASP F 60 " pdb=" CG ASP F 60 " pdb=" OD1 ASP F 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.94 57.94 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP D 60 " pdb=" CB ASP D 60 " pdb=" CG ASP D 60 " pdb=" OD1 ASP D 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.94 57.94 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 3027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 209 0.050 - 0.101: 202 0.101 - 0.151: 129 0.151 - 0.201: 54 0.201 - 0.252: 24 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA GLU L 9 " pdb=" N GLU L 9 " pdb=" C GLU L 9 " pdb=" CB GLU L 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU F 9 " pdb=" N GLU F 9 " pdb=" C GLU F 9 " pdb=" CB GLU F 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU H 9 " pdb=" N GLU H 9 " pdb=" C GLU H 9 " pdb=" CB GLU H 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 615 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 10 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ALA B 10 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA B 10 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE B 11 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 10 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C ALA D 10 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA D 10 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE D 11 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 10 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ALA J 10 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA J 10 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE J 11 " -0.018 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2588 2.99 - 3.47: 4931 3.47 - 3.94: 9219 3.94 - 4.42: 10402 4.42 - 4.90: 19642 Nonbonded interactions: 46782 Sorted by model distance: nonbonded pdb=" OD2 ASP H 33 " pdb=" N SER K 2 " model vdw 2.509 2.520 nonbonded pdb=" OD2 ASP F 33 " pdb=" N SER I 2 " model vdw 2.509 2.520 nonbonded pdb=" OD2 ASP B 33 " pdb=" N SER E 2 " model vdw 2.509 2.520 nonbonded pdb=" OD2 ASP D 33 " pdb=" N SER G 2 " model vdw 2.509 2.520 nonbonded pdb=" N PHE A 36 " pdb=" O PHE A 36 " model vdw 2.526 2.496 ... (remaining 46777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.620 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 17.940 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.051 5394 Z= 0.837 Angle : 1.999 7.348 7218 Z= 1.464 Chirality : 0.100 0.252 618 Planarity : 0.010 0.030 972 Dihedral : 15.174 87.747 1878 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP A 18 HIS 0.002 0.001 HIS G 37 PHE 0.021 0.003 PHE K 36 TYR 0.009 0.003 TYR C 21 ARG 0.003 0.001 ARG J 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.597 Fit side-chains REVERT: B 3 PHE cc_start: 0.6667 (m-10) cc_final: 0.6453 (m-80) REVERT: B 24 MET cc_start: 0.7434 (mmm) cc_final: 0.6930 (mtm) REVERT: B 39 ARG cc_start: 0.6256 (ttt180) cc_final: 0.5382 (ttt90) REVERT: B 56 GLU cc_start: 0.7174 (tt0) cc_final: 0.6770 (mt-10) REVERT: B 58 ILE cc_start: 0.7441 (mt) cc_final: 0.7124 (mp) REVERT: B 67 ARG cc_start: 0.7076 (mtt180) cc_final: 0.5907 (ttt-90) REVERT: A 12 ASP cc_start: 0.7747 (t70) cc_final: 0.7159 (m-30) REVERT: A 19 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6914 (ttm110) REVERT: A 26 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6543 (mt-10) REVERT: A 33 ASP cc_start: 0.6762 (m-30) cc_final: 0.6500 (m-30) REVERT: D 19 ARG cc_start: 0.6184 (mtt180) cc_final: 0.5875 (mtt90) REVERT: D 67 ARG cc_start: 0.5640 (mtt180) cc_final: 0.4634 (tmt90) REVERT: C 18 TRP cc_start: 0.6658 (t60) cc_final: 0.6105 (t60) REVERT: C 19 ARG cc_start: 0.6388 (mtt180) cc_final: 0.5566 (ttm-80) REVERT: C 24 MET cc_start: 0.6708 (mtt) cc_final: 0.6393 (mmm) REVERT: F 56 GLU cc_start: 0.6344 (tt0) cc_final: 0.5659 (mt-10) REVERT: F 58 ILE cc_start: 0.5875 (mt) cc_final: 0.5612 (mp) REVERT: F 67 ARG cc_start: 0.5810 (mtt180) cc_final: 0.4816 (tmt90) REVERT: E 19 ARG cc_start: 0.6107 (mtt180) cc_final: 0.5839 (ttm170) REVERT: E 24 MET cc_start: 0.6857 (mtt) cc_final: 0.6599 (mtp) REVERT: E 32 SER cc_start: 0.6455 (p) cc_final: 0.6221 (m) REVERT: H 26 GLU cc_start: 0.5532 (mt-10) cc_final: 0.5211 (mt-10) REVERT: H 63 GLU cc_start: 0.6532 (tt0) cc_final: 0.6315 (tt0) REVERT: H 67 ARG cc_start: 0.5664 (mtt180) cc_final: 0.4591 (tmt90) REVERT: G 24 MET cc_start: 0.6749 (mtt) cc_final: 0.6336 (mmm) REVERT: G 26 GLU cc_start: 0.5505 (mt-10) cc_final: 0.5302 (mt-10) REVERT: G 32 SER cc_start: 0.6653 (p) cc_final: 0.6398 (m) REVERT: J 26 GLU cc_start: 0.5319 (mt-10) cc_final: 0.5023 (mt-10) REVERT: J 56 GLU cc_start: 0.6374 (tt0) cc_final: 0.5732 (mt-10) REVERT: J 58 ILE cc_start: 0.6028 (mt) cc_final: 0.5717 (mp) REVERT: J 67 ARG cc_start: 0.5572 (mtt180) cc_final: 0.4321 (tmt90) REVERT: I 12 ASP cc_start: 0.6837 (t70) cc_final: 0.6189 (m-30) REVERT: I 19 ARG cc_start: 0.6062 (mtt180) cc_final: 0.5739 (ttm110) REVERT: I 25 ARG cc_start: 0.5714 (mtt180) cc_final: 0.5456 (mtm-85) REVERT: I 26 GLU cc_start: 0.5572 (mt-10) cc_final: 0.5259 (mt-10) REVERT: L 9 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5568 (tt0) REVERT: L 23 ASP cc_start: 0.7195 (t0) cc_final: 0.6976 (t0) REVERT: L 39 ARG cc_start: 0.6916 (ttt180) cc_final: 0.6507 (ttp-170) REVERT: L 63 GLU cc_start: 0.6438 (tt0) cc_final: 0.6135 (tt0) REVERT: L 67 ARG cc_start: 0.6131 (mtt180) cc_final: 0.5120 (ttt90) REVERT: K 12 ASP cc_start: 0.7078 (t70) cc_final: 0.6431 (m-30) REVERT: K 22 SER cc_start: 0.7753 (p) cc_final: 0.7337 (t) REVERT: K 23 ASP cc_start: 0.6222 (t0) cc_final: 0.4794 (t0) REVERT: K 24 MET cc_start: 0.7613 (mtt) cc_final: 0.6947 (mmm) REVERT: K 25 ARG cc_start: 0.6168 (mtt180) cc_final: 0.5112 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 1.3525 time to fit residues: 330.9465 Evaluate side-chains 178 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN K 37 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5394 Z= 0.167 Angle : 0.549 6.826 7218 Z= 0.309 Chirality : 0.039 0.144 618 Planarity : 0.003 0.030 972 Dihedral : 4.593 13.200 738 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.67 % Allowed : 19.79 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.27), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 18 HIS 0.005 0.001 HIS G 37 PHE 0.024 0.002 PHE E 36 TYR 0.016 0.002 TYR F 42 ARG 0.004 0.000 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 0.605 Fit side-chains REVERT: B 39 ARG cc_start: 0.6295 (ttt180) cc_final: 0.5349 (ttt90) REVERT: B 46 LYS cc_start: 0.6208 (mttt) cc_final: 0.5906 (mtpm) REVERT: B 67 ARG cc_start: 0.7199 (mtt180) cc_final: 0.5873 (tmt90) REVERT: A 17 MET cc_start: 0.6942 (ttp) cc_final: 0.6577 (ttp) REVERT: A 19 ARG cc_start: 0.7344 (mtt180) cc_final: 0.6862 (ttm110) REVERT: A 21 TYR cc_start: 0.6214 (m-80) cc_final: 0.5921 (m-80) REVERT: D 17 MET cc_start: 0.7826 (mmp) cc_final: 0.7224 (mmp) REVERT: D 19 ARG cc_start: 0.6138 (mtt180) cc_final: 0.5671 (mtt90) REVERT: D 67 ARG cc_start: 0.5626 (mtt180) cc_final: 0.4646 (tmt90) REVERT: C 18 TRP cc_start: 0.6668 (t60) cc_final: 0.6300 (t60) REVERT: C 19 ARG cc_start: 0.5897 (mtt180) cc_final: 0.5590 (ttm-80) REVERT: F 56 GLU cc_start: 0.6057 (tt0) cc_final: 0.5578 (mt-10) REVERT: F 58 ILE cc_start: 0.5732 (mt) cc_final: 0.5512 (mp) REVERT: F 67 ARG cc_start: 0.5854 (mtt180) cc_final: 0.4796 (ttt90) REVERT: E 24 MET cc_start: 0.7633 (mtt) cc_final: 0.7327 (mtp) REVERT: H 39 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5986 (ttt90) REVERT: H 46 LYS cc_start: 0.6341 (mttt) cc_final: 0.5981 (mtpm) REVERT: H 67 ARG cc_start: 0.5639 (mtt180) cc_final: 0.4526 (ttt90) REVERT: G 21 TYR cc_start: 0.5440 (m-80) cc_final: 0.5086 (m-80) REVERT: J 39 ARG cc_start: 0.5946 (ttt180) cc_final: 0.5551 (ttt90) REVERT: J 42 TYR cc_start: 0.6753 (t80) cc_final: 0.6480 (t80) REVERT: J 58 ILE cc_start: 0.5794 (mt) cc_final: 0.5528 (mp) REVERT: L 46 LYS cc_start: 0.7518 (mttt) cc_final: 0.7295 (tppt) REVERT: L 63 GLU cc_start: 0.6216 (tt0) cc_final: 0.5903 (tt0) REVERT: L 67 ARG cc_start: 0.6010 (mtt180) cc_final: 0.5029 (ttt90) REVERT: K 5 SER cc_start: 0.6815 (t) cc_final: 0.6580 (p) REVERT: K 22 SER cc_start: 0.8129 (p) cc_final: 0.7815 (t) REVERT: K 23 ASP cc_start: 0.6197 (t0) cc_final: 0.4609 (t0) REVERT: K 24 MET cc_start: 0.7892 (mtt) cc_final: 0.7295 (mtm) REVERT: K 25 ARG cc_start: 0.6187 (mtt180) cc_final: 0.5140 (mmt180) REVERT: K 34 LYS cc_start: 0.6140 (tttt) cc_final: 0.5077 (tptp) outliers start: 8 outliers final: 6 residues processed: 166 average time/residue: 1.3731 time to fit residues: 235.7915 Evaluate side-chains 151 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 5394 Z= 0.512 Angle : 0.732 8.005 7218 Z= 0.418 Chirality : 0.044 0.126 618 Planarity : 0.005 0.035 972 Dihedral : 6.300 22.920 738 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.00 % Allowed : 19.58 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 18 HIS 0.004 0.001 HIS L 37 PHE 0.037 0.004 PHE F 6 TYR 0.020 0.002 TYR C 29 ARG 0.006 0.001 ARG K 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7816 (t) cc_final: 0.7198 (p) REVERT: A 17 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6852 (ttp) REVERT: D 3 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.6223 (m-10) REVERT: D 17 MET cc_start: 0.7434 (mmp) cc_final: 0.6834 (mmp) REVERT: D 39 ARG cc_start: 0.5892 (ttm170) cc_final: 0.5292 (ttp-170) REVERT: D 67 ARG cc_start: 0.5858 (mtt180) cc_final: 0.5642 (mmm-85) REVERT: C 12 ASP cc_start: 0.6698 (t0) cc_final: 0.6396 (t0) REVERT: F 47 ARG cc_start: 0.6666 (tpp-160) cc_final: 0.6219 (mmt180) REVERT: E 24 MET cc_start: 0.7657 (mtt) cc_final: 0.7422 (mtp) REVERT: H 16 ASP cc_start: 0.6671 (t0) cc_final: 0.6438 (t0) REVERT: H 47 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.5980 (mtm-85) REVERT: G 12 ASP cc_start: 0.6728 (t0) cc_final: 0.6515 (t0) REVERT: G 34 LYS cc_start: 0.5424 (tttt) cc_final: 0.4796 (mttt) REVERT: J 67 ARG cc_start: 0.5691 (mtt180) cc_final: 0.5386 (mtm-85) REVERT: L 39 ARG cc_start: 0.6922 (ttt180) cc_final: 0.6374 (ttp-170) REVERT: L 47 ARG cc_start: 0.7045 (mpt180) cc_final: 0.6694 (tpt170) REVERT: L 63 GLU cc_start: 0.6068 (tt0) cc_final: 0.5840 (tt0) REVERT: K 9 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6560 (mm-30) REVERT: K 12 ASP cc_start: 0.6650 (t0) cc_final: 0.6057 (m-30) REVERT: K 24 MET cc_start: 0.7681 (mtt) cc_final: 0.7428 (mtm) REVERT: K 34 LYS cc_start: 0.5740 (tttt) cc_final: 0.4846 (tmtt) outliers start: 24 outliers final: 9 residues processed: 182 average time/residue: 1.4693 time to fit residues: 275.9180 Evaluate side-chains 172 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5394 Z= 0.398 Angle : 0.664 7.660 7218 Z= 0.377 Chirality : 0.042 0.141 618 Planarity : 0.004 0.026 972 Dihedral : 6.058 20.646 738 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 6.46 % Allowed : 19.79 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 18 HIS 0.003 0.001 HIS L 37 PHE 0.026 0.003 PHE F 6 TYR 0.013 0.002 TYR K 21 ARG 0.004 0.001 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7769 (t) cc_final: 0.7218 (p) REVERT: A 2 SER cc_start: 0.7364 (p) cc_final: 0.7046 (p) REVERT: A 17 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7127 (ttp) REVERT: D 3 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6151 (m-80) REVERT: D 17 MET cc_start: 0.7467 (mmp) cc_final: 0.6789 (mmp) REVERT: D 63 GLU cc_start: 0.5898 (tt0) cc_final: 0.5523 (mt-10) REVERT: D 67 ARG cc_start: 0.5792 (mtt180) cc_final: 0.5575 (mmm-85) REVERT: C 12 ASP cc_start: 0.6776 (t0) cc_final: 0.6444 (t0) REVERT: C 19 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5492 (ttp-170) REVERT: F 33 ASP cc_start: 0.7041 (m-30) cc_final: 0.6666 (m-30) REVERT: F 47 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5971 (mmt180) REVERT: E 24 MET cc_start: 0.7735 (mtt) cc_final: 0.7502 (mtp) REVERT: H 3 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.5654 (m-80) REVERT: H 47 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.5928 (mtm-85) REVERT: H 63 GLU cc_start: 0.5780 (tt0) cc_final: 0.5347 (mt-10) REVERT: G 12 ASP cc_start: 0.6732 (t70) cc_final: 0.6502 (t0) REVERT: G 34 LYS cc_start: 0.5395 (tttt) cc_final: 0.4786 (mttt) REVERT: L 39 ARG cc_start: 0.6973 (ttt180) cc_final: 0.6437 (ttp-170) REVERT: L 47 ARG cc_start: 0.6981 (mpt180) cc_final: 0.6662 (mpt90) REVERT: K 5 SER cc_start: 0.7184 (t) cc_final: 0.6816 (p) REVERT: K 9 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6549 (mm-30) REVERT: K 24 MET cc_start: 0.7667 (mtt) cc_final: 0.7458 (mtm) REVERT: K 25 ARG cc_start: 0.6529 (mtt90) cc_final: 0.4825 (mmt180) REVERT: K 34 LYS cc_start: 0.5654 (tttt) cc_final: 0.4797 (tptp) outliers start: 31 outliers final: 15 residues processed: 184 average time/residue: 1.4830 time to fit residues: 281.6285 Evaluate side-chains 186 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 16 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5398 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5394 Z= 0.240 Angle : 0.575 7.564 7218 Z= 0.321 Chirality : 0.039 0.130 618 Planarity : 0.003 0.026 972 Dihedral : 5.423 17.642 738 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.62 % Allowed : 21.88 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 18 HIS 0.003 0.001 HIS G 37 PHE 0.020 0.002 PHE E 36 TYR 0.011 0.001 TYR F 42 ARG 0.003 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7811 (t) cc_final: 0.7279 (p) REVERT: B 33 ASP cc_start: 0.7239 (m-30) cc_final: 0.7014 (m-30) REVERT: B 63 GLU cc_start: 0.7248 (tt0) cc_final: 0.6587 (mt-10) REVERT: A 2 SER cc_start: 0.7390 (p) cc_final: 0.7078 (p) REVERT: A 17 MET cc_start: 0.7467 (ttp) cc_final: 0.7168 (ttp) REVERT: D 63 GLU cc_start: 0.5927 (tt0) cc_final: 0.5529 (mt-10) REVERT: D 67 ARG cc_start: 0.5826 (mtt180) cc_final: 0.5614 (mmm-85) REVERT: C 12 ASP cc_start: 0.6719 (t0) cc_final: 0.6305 (t0) REVERT: C 19 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5487 (ttp-170) REVERT: F 47 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.6188 (mpt180) REVERT: E 24 MET cc_start: 0.7621 (mtt) cc_final: 0.7372 (mtp) REVERT: H 3 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: H 47 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.5865 (mtm-85) REVERT: H 63 GLU cc_start: 0.5846 (tt0) cc_final: 0.5388 (mt-10) REVERT: G 12 ASP cc_start: 0.6819 (t70) cc_final: 0.6529 (t0) REVERT: G 34 LYS cc_start: 0.5361 (tttt) cc_final: 0.4766 (mttt) REVERT: J 63 GLU cc_start: 0.5545 (tt0) cc_final: 0.5206 (mt-10) REVERT: L 39 ARG cc_start: 0.7000 (ttt180) cc_final: 0.6454 (ttp-170) REVERT: L 63 GLU cc_start: 0.5866 (tt0) cc_final: 0.5223 (mt-10) REVERT: K 5 SER cc_start: 0.7320 (t) cc_final: 0.6948 (p) REVERT: K 9 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6560 (mm-30) REVERT: K 34 LYS cc_start: 0.5667 (tttt) cc_final: 0.4791 (tptp) outliers start: 27 outliers final: 13 residues processed: 173 average time/residue: 1.4256 time to fit residues: 254.5918 Evaluate side-chains 180 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 16 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5394 Z= 0.474 Angle : 0.718 8.901 7218 Z= 0.405 Chirality : 0.043 0.158 618 Planarity : 0.004 0.037 972 Dihedral : 6.309 22.826 738 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 6.25 % Allowed : 22.50 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 18 HIS 0.007 0.001 HIS G 37 PHE 0.025 0.003 PHE J 6 TYR 0.012 0.002 TYR J 35 ARG 0.004 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.7208 (mmp) cc_final: 0.6963 (mmm) REVERT: B 22 SER cc_start: 0.7626 (t) cc_final: 0.7095 (p) REVERT: A 2 SER cc_start: 0.7334 (p) cc_final: 0.7128 (p) REVERT: A 17 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7011 (ttp) REVERT: D 3 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: D 32 SER cc_start: 0.6415 (t) cc_final: 0.6090 (m) REVERT: D 39 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5381 (ttp-170) REVERT: D 63 GLU cc_start: 0.5896 (tt0) cc_final: 0.5520 (mt-10) REVERT: C 12 ASP cc_start: 0.6712 (t0) cc_final: 0.6290 (t0) REVERT: C 19 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5344 (ttt-90) REVERT: F 47 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5964 (mmt180) REVERT: E 24 MET cc_start: 0.7601 (mtt) cc_final: 0.7363 (mtp) REVERT: H 3 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5461 (m-80) REVERT: H 47 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5880 (mtm-85) REVERT: H 63 GLU cc_start: 0.5869 (tt0) cc_final: 0.5432 (mt-10) REVERT: G 12 ASP cc_start: 0.6750 (t70) cc_final: 0.6492 (t0) REVERT: G 34 LYS cc_start: 0.5378 (tttt) cc_final: 0.4877 (mttt) REVERT: J 63 GLU cc_start: 0.5550 (tt0) cc_final: 0.5148 (mt-10) REVERT: I 26 GLU cc_start: 0.4929 (mt-10) cc_final: 0.4633 (mt-10) REVERT: L 39 ARG cc_start: 0.7041 (ttt180) cc_final: 0.6486 (ttp-170) REVERT: L 63 GLU cc_start: 0.5745 (tt0) cc_final: 0.5169 (mt-10) REVERT: K 5 SER cc_start: 0.7314 (t) cc_final: 0.6929 (p) REVERT: K 9 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6522 (mm-30) REVERT: K 34 LYS cc_start: 0.5350 (tttt) cc_final: 0.4585 (tmtt) outliers start: 30 outliers final: 14 residues processed: 185 average time/residue: 1.4553 time to fit residues: 277.9439 Evaluate side-chains 190 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 16 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5394 Z= 0.174 Angle : 0.555 8.486 7218 Z= 0.303 Chirality : 0.038 0.131 618 Planarity : 0.002 0.021 972 Dihedral : 5.076 16.354 738 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.75 % Allowed : 25.21 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 18 HIS 0.003 0.001 HIS G 37 PHE 0.019 0.002 PHE I 36 TYR 0.011 0.001 TYR F 42 ARG 0.005 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7757 (t) cc_final: 0.7231 (p) REVERT: B 63 GLU cc_start: 0.7196 (tt0) cc_final: 0.6761 (mt-10) REVERT: A 2 SER cc_start: 0.7426 (p) cc_final: 0.7158 (p) REVERT: A 17 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7131 (ttp) REVERT: D 63 GLU cc_start: 0.5742 (tt0) cc_final: 0.5479 (mt-10) REVERT: C 19 ARG cc_start: 0.6053 (OUTLIER) cc_final: 0.5484 (ttp-170) REVERT: F 33 ASP cc_start: 0.7036 (m-30) cc_final: 0.6831 (m-30) REVERT: F 63 GLU cc_start: 0.5328 (tt0) cc_final: 0.5047 (mt-10) REVERT: H 16 ASP cc_start: 0.6588 (t0) cc_final: 0.5500 (t0) REVERT: H 47 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5552 (mtm-85) REVERT: H 63 GLU cc_start: 0.5808 (tt0) cc_final: 0.5449 (mt-10) REVERT: G 12 ASP cc_start: 0.6871 (t70) cc_final: 0.6580 (t0) REVERT: G 34 LYS cc_start: 0.5309 (tttt) cc_final: 0.4810 (mttt) REVERT: J 63 GLU cc_start: 0.5593 (tt0) cc_final: 0.5276 (mt-10) REVERT: L 39 ARG cc_start: 0.7034 (ttt180) cc_final: 0.6471 (ttp-170) REVERT: L 63 GLU cc_start: 0.5879 (tt0) cc_final: 0.5337 (mt-10) REVERT: K 5 SER cc_start: 0.7271 (t) cc_final: 0.6892 (p) REVERT: K 9 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6428 (mm-30) REVERT: K 25 ARG cc_start: 0.6487 (mtt90) cc_final: 0.4796 (mmt-90) REVERT: K 34 LYS cc_start: 0.5682 (tttt) cc_final: 0.4794 (tptp) outliers start: 18 outliers final: 7 residues processed: 164 average time/residue: 1.4841 time to fit residues: 251.1447 Evaluate side-chains 165 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 16 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5394 Z= 0.170 Angle : 0.541 8.769 7218 Z= 0.293 Chirality : 0.038 0.128 618 Planarity : 0.002 0.033 972 Dihedral : 4.890 14.360 738 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.33 % Allowed : 26.67 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 18 HIS 0.003 0.001 HIS K 37 PHE 0.018 0.002 PHE I 36 TYR 0.013 0.001 TYR H 42 ARG 0.007 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7722 (t) cc_final: 0.7209 (p) REVERT: B 63 GLU cc_start: 0.7149 (tt0) cc_final: 0.6769 (mt-10) REVERT: A 2 SER cc_start: 0.7383 (p) cc_final: 0.7116 (p) REVERT: A 17 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7135 (ttp) REVERT: A 19 ARG cc_start: 0.6892 (ttt180) cc_final: 0.6545 (ttm170) REVERT: D 63 GLU cc_start: 0.5736 (tt0) cc_final: 0.5514 (mt-10) REVERT: C 19 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5318 (ttp-110) REVERT: F 33 ASP cc_start: 0.6808 (m-30) cc_final: 0.6569 (m-30) REVERT: F 63 GLU cc_start: 0.5234 (tt0) cc_final: 0.5017 (mt-10) REVERT: H 47 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.5368 (mtm-85) REVERT: H 63 GLU cc_start: 0.5796 (tt0) cc_final: 0.5451 (mt-10) REVERT: G 12 ASP cc_start: 0.6921 (t70) cc_final: 0.6566 (t0) REVERT: G 34 LYS cc_start: 0.5306 (tttt) cc_final: 0.4839 (mttt) REVERT: J 63 GLU cc_start: 0.5604 (tt0) cc_final: 0.5292 (mt-10) REVERT: I 12 ASP cc_start: 0.6973 (t0) cc_final: 0.6348 (m-30) REVERT: L 39 ARG cc_start: 0.7099 (ttt180) cc_final: 0.6480 (ttp-170) REVERT: L 63 GLU cc_start: 0.5748 (tt0) cc_final: 0.5243 (mt-10) REVERT: K 5 SER cc_start: 0.7244 (t) cc_final: 0.6871 (p) REVERT: K 9 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6399 (mm-30) REVERT: K 25 ARG cc_start: 0.6486 (mtt90) cc_final: 0.4790 (mmt-90) REVERT: K 34 LYS cc_start: 0.5469 (tttt) cc_final: 0.4613 (tptp) outliers start: 16 outliers final: 5 residues processed: 159 average time/residue: 1.5169 time to fit residues: 248.7797 Evaluate side-chains 161 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5394 Z= 0.472 Angle : 0.730 9.762 7218 Z= 0.406 Chirality : 0.043 0.157 618 Planarity : 0.004 0.035 972 Dihedral : 6.130 21.810 738 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.96 % Allowed : 26.88 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.24), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.18), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 18 HIS 0.005 0.001 HIS G 37 PHE 0.033 0.003 PHE F 3 TYR 0.014 0.002 TYR B 35 ARG 0.008 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7605 (t) cc_final: 0.7060 (p) REVERT: B 63 GLU cc_start: 0.7239 (tt0) cc_final: 0.6757 (mt-10) REVERT: A 2 SER cc_start: 0.7380 (p) cc_final: 0.7145 (p) REVERT: A 17 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.7001 (ttp) REVERT: D 3 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: D 32 SER cc_start: 0.6718 (t) cc_final: 0.6274 (m) REVERT: D 63 GLU cc_start: 0.5706 (tt0) cc_final: 0.5463 (mt-10) REVERT: C 12 ASP cc_start: 0.6745 (t0) cc_final: 0.6263 (t0) REVERT: C 19 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5376 (ttt-90) REVERT: F 42 TYR cc_start: 0.6822 (t80) cc_final: 0.6582 (t80) REVERT: F 63 GLU cc_start: 0.5019 (tt0) cc_final: 0.4754 (mt-10) REVERT: H 3 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: H 47 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.5786 (mtm-85) REVERT: H 63 GLU cc_start: 0.5856 (tt0) cc_final: 0.5477 (mt-10) REVERT: G 12 ASP cc_start: 0.6839 (t70) cc_final: 0.6496 (t0) REVERT: G 34 LYS cc_start: 0.5304 (tttt) cc_final: 0.4842 (mttt) REVERT: J 26 GLU cc_start: 0.5426 (OUTLIER) cc_final: 0.5180 (mt-10) REVERT: J 63 GLU cc_start: 0.5479 (tt0) cc_final: 0.5212 (mt-10) REVERT: I 12 ASP cc_start: 0.6821 (t0) cc_final: 0.6188 (m-30) REVERT: L 39 ARG cc_start: 0.7061 (ttt180) cc_final: 0.6494 (ttp-170) REVERT: L 63 GLU cc_start: 0.5741 (tt0) cc_final: 0.5131 (mt-10) REVERT: K 5 SER cc_start: 0.7239 (t) cc_final: 0.6871 (p) REVERT: K 9 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6521 (mm-30) REVERT: K 34 LYS cc_start: 0.4998 (tttt) cc_final: 0.4397 (mttt) outliers start: 19 outliers final: 9 residues processed: 172 average time/residue: 1.4827 time to fit residues: 263.0711 Evaluate side-chains 179 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5394 Z= 0.161 Angle : 0.555 9.113 7218 Z= 0.299 Chirality : 0.038 0.128 618 Planarity : 0.002 0.033 972 Dihedral : 4.922 18.107 738 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.29 % Allowed : 28.33 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 18 HIS 0.002 0.001 HIS G 37 PHE 0.020 0.002 PHE H 3 TYR 0.013 0.001 TYR F 42 ARG 0.007 0.000 ARG A 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 SER cc_start: 0.7719 (t) cc_final: 0.7179 (p) REVERT: B 59 SER cc_start: 0.6753 (m) cc_final: 0.6300 (t) REVERT: B 63 GLU cc_start: 0.7185 (tt0) cc_final: 0.6843 (mt-10) REVERT: A 2 SER cc_start: 0.7415 (p) cc_final: 0.7134 (p) REVERT: A 17 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7134 (ttp) REVERT: A 19 ARG cc_start: 0.6894 (ttt180) cc_final: 0.6581 (ttm170) REVERT: D 63 GLU cc_start: 0.5795 (tt0) cc_final: 0.5594 (mt-10) REVERT: C 19 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5425 (ttp-110) REVERT: F 42 TYR cc_start: 0.6890 (t80) cc_final: 0.6656 (t80) REVERT: H 3 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: H 47 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5377 (mtm-85) REVERT: H 63 GLU cc_start: 0.5727 (tt0) cc_final: 0.5460 (mt-10) REVERT: G 12 ASP cc_start: 0.6920 (t70) cc_final: 0.6631 (t0) REVERT: G 34 LYS cc_start: 0.5219 (tttt) cc_final: 0.4734 (mttt) REVERT: J 56 GLU cc_start: 0.6721 (tt0) cc_final: 0.6498 (tt0) REVERT: J 63 GLU cc_start: 0.5555 (tt0) cc_final: 0.5269 (mt-10) REVERT: L 39 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6511 (ttp-170) REVERT: L 63 GLU cc_start: 0.5786 (tt0) cc_final: 0.5299 (mt-10) REVERT: K 5 SER cc_start: 0.7223 (t) cc_final: 0.6879 (p) REVERT: K 25 ARG cc_start: 0.6493 (mtt90) cc_final: 0.4814 (mmt-90) REVERT: K 34 LYS cc_start: 0.5096 (tttt) cc_final: 0.4451 (mttt) outliers start: 11 outliers final: 4 residues processed: 154 average time/residue: 1.4422 time to fit residues: 229.2941 Evaluate side-chains 158 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN F 28 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN H 28 ASN ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.133434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.112316 restraints weight = 6166.935| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.03 r_work: 0.3605 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5394 Z= 0.365 Angle : 0.681 10.535 7218 Z= 0.374 Chirality : 0.041 0.143 618 Planarity : 0.004 0.034 972 Dihedral : 5.781 19.795 738 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.75 % Allowed : 28.54 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.24), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 18 HIS 0.004 0.001 HIS G 37 PHE 0.040 0.003 PHE F 3 TYR 0.013 0.002 TYR F 42 ARG 0.008 0.000 ARG A 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3862.33 seconds wall clock time: 68 minutes 15.93 seconds (4095.93 seconds total)